Variant report

Variant	rs72960709
Chromosome Location	chr2:99487380-99487381
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RAD21	chr2:99487351-99487481	IMR90	lung:	n/a	n/a
2	CHD2	chr2:99487324-99487527	K562	blood:	n/a	n/a
3	CTCF	chr2:99487203-99487551	H1-hESC	embryonic stem cell:	n/a	chr2:99487471-99487479
4	CTCF	chr2:99487287-99487468	K562	blood:	n/a	n/a
5	RAD21	chr2:99487230-99487586	H1-hESC	embryonic stem cell:	n/a	n/a
6	RAD21	chr2:99487306-99487457	K562	blood:	n/a	n/a
7	RAD21	chr2:99487177-99487523	H1-hESC	embryonic stem cell:	n/a	n/a
8	RAD21	chr2:99487218-99487562	HepG2	liver:	n/a	n/a
9	CTCF	chr2:99487311-99487498	H1-hESC	embryonic stem cell:	n/a	chr2:99487471-99487479
10	CTCF	chr2:99487360-99487510	HepG2	liver:	n/a	chr2:99487471-99487479
11	CTCF	chr2:99487286-99487594	K562	blood:	n/a	chr2:99487471-99487479
12	RAD21	chr2:99487175-99487615	H1-hESC	embryonic stem cell:	n/a	n/a
13	CTCF	chr2:99487269-99487557	K562	blood:	n/a	chr2:99487471-99487479
14	CTCF	chr2:99487320-99487470	WI-38	lung:	n/a	n/a
15	CTCF	chr2:99487335-99487466	HepG2	liver:	n/a	n/a
16	CTCF	chr2:99487360-99487510	K562	blood:	n/a	chr2:99487471-99487479
17	CTCF	chr2:99487354-99487435	HepG2	liver:	n/a	n/a
18	CTCF	chr2:99487320-99487470	K562	blood:	n/a	n/a
19	CTCF	chr2:99487320-99487508	K562	blood:	n/a	chr2:99487471-99487479
20	RAD21	chr2:99487329-99487474	K562	blood:	n/a	n/a
21	CTCF	chr2:99487269-99487472	H1-hESC	embryonic stem cell:	n/a	n/a
22	CTCF	chr2:99487240-99487390	A549	lung:	n/a	n/a
23	CTCF	chr2:99487340-99487490	HBMEC	blood vessel:	n/a	chr2:99487471-99487479
24	RCOR1	chr2:99487354-99487474	K562	blood:	n/a	n/a
25	CTCF	chr2:99487326-99487499	Fibrobl	skin:	n/a	chr2:99487471-99487479
26	RAD21	chr2:99487261-99487492	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:99485026..99487433-chr2:100105196..100107704,3	MCF-7	breast:
2	chr2:99484412..99487919-chr2:99523957..99528531,6	MCF-7	breast:

Variant related genes	Relation type
KIAA1211L	TF binding region
ENSG00000135945	Chromatin interaction
ENSG00000196872	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs56923186	1.00[AMR][1000 genomes]
rs58738020	1.00[AMR][1000 genomes]
rs58821307	1.00[AMR][1000 genomes]
rs59365702	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60523550	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60725966	1.00[AMR][1000 genomes]
rs60745907	1.00[AMR][1000 genomes]
rs61503115	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72956638	1.00[AMR][1000 genomes]
rs72956659	1.00[AMR][1000 genomes]
rs72956663	1.00[AMR][1000 genomes]
rs72957625	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72957633	1.00[AMR][1000 genomes]
rs72957643	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72957654	1.00[AMR][1000 genomes]
rs72957656	1.00[AMR][1000 genomes]
rs72957660	1.00[AMR][1000 genomes]
rs72957672	1.00[AMR][1000 genomes]
rs72958630	1.00[AMR][1000 genomes]
rs72958634	1.00[AMR][1000 genomes]
rs72958636	1.00[AMR][1000 genomes]
rs72958646	1.00[AMR][1000 genomes]
rs72958649	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72958653	1.00[AMR][1000 genomes]
rs72958659	1.00[AMR][1000 genomes]
rs72958661	1.00[AMR][1000 genomes]
rs72958666	1.00[AMR][1000 genomes]
rs73965241	1.00[AMR][1000 genomes]
rs73965242	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011278	chr2:99280928-99638376	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv535835	chr2:99280928-99638376	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv582517	chr2:99440917-99487972	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99484000-99489000	Weak transcription	Stomach Smooth Muscle	stomach
2	chr2:99485000-99488200	Enhancers	Fetal Muscle Leg	muscle
3	chr2:99485200-99487400	Weak transcription	Brain Angular Gyrus	brain
4	chr2:99485200-99487800	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr2:99485400-99487400	Enhancers	Fetal Muscle Trunk	muscle
6	chr2:99485600-99499800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr2:99485800-99488200	Enhancers	Cortex derived primary cultured neurospheres	brain
8	chr2:99485800-99491800	Weak transcription	Brain Anterior Caudate	brain
9	chr2:99486000-99487600	Enhancers	Fetal Thymus	thymus
10	chr2:99486000-99488600	Weak transcription	Right Atrium	heart
11	chr2:99486200-99487600	Enhancers	Skeletal Muscle Female	skeletal muscle
12	chr2:99486200-99487800	Enhancers	Skeletal Muscle Male	skeletal muscle
13	chr2:99486200-99489800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr2:99486400-99487400	Enhancers	Fetal Intestine Small	intestine
15	chr2:99486400-99487800	Enhancers	Stomach Mucosa	stomach
16	chr2:99486400-99488000	Enhancers	Esophagus	oesophagus
17	chr2:99486400-99489600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr2:99486600-99487600	Enhancers	Pancreas	Pancrea
19	chr2:99486600-99487600	Enhancers	Rectal Mucosa Donor 31	rectum
20	chr2:99486600-99489400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr2:99486600-99489800	Weak transcription	NHEK	skin
22	chr2:99486800-99487400	Enhancers	Colonic Mucosa	Colon
23	chr2:99486800-99489600	Weak transcription	Placenta	Placenta
24	chr2:99486800-99491000	Weak transcription	GM12878-XiMat	blood
25	chr2:99487000-99487400	Enhancers	Lung	lung
26	chr2:99487000-99487400	Enhancers	Rectal Mucosa Donor 29	rectum
27	chr2:99487000-99487600	Enhancers	Duodenum Mucosa	Duodenum
28	chr2:99487000-99487600	Enhancers	Gastric	stomach
29	chr2:99487000-99489600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr2:99487000-99489600	Weak transcription	HMEC	breast

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